SBW25

Experimenting with the tripalv3 JSON+LD API Introduction In this post I'm experimenting with querying the JSON-LD (LD stands for Linked Data) API of my Tripal3 genome database for Pseudomonas fluorescens SBW25. A little bit of background: Tripal is a content management system (CMS) for genomic data, based on the Drupal CMS framework. It facilitates setting up customized genomic database webservers to publish genome assemblies, annotation tracks, experimental and modeling data for one or several organisms. [Read More]

Introduction In this post I will present example SPARQL queries against the Pseudomonas fluorescens SBW25 knowledge graph (SBW25KG). The knowlegde graph was derived from the manually created annotation in gff3 format, as explained in a previous post. The queries are run against a local instance of the apache-jena-fuseki triplestore. First, I set the endpoint URL and the maximum number of returned records: %endpoint http://micropop046:3030/plu/ %show 50 Endpoint set to: http://micropop046:3030/plu/Result maximum size: 50 Retrieve 10 CDS’s from the SBW25KG. [Read More]

Introduction In this article, I will describe the steps taken to generate a RDF (Resource Description Format) datastructure starting from a gff3 formatted genome annotation file. The annotation file in question is the new reference annotation for Pseudomonas fluorescens strain SBW25. Required packages I will make use of the following python packages: gffutils to read the gff3 file into a sqlite database. rdflib to construct the rdf graph. requests to fetch data (e. [Read More]